Netter: re-ranking gene network inference predictions using structural network properties

Background: Many algorithms have been developed to infer the topology of gene regulatory networks from gene expression data. These methods typically produce a ranking of links between genes with associated confidence scores, after which a certain threshold is chosen to produce the inferred topology. However, the structural properties of the predicted network do not resemble those typical for a gene regulatory network, as most algorithms only take into account connections found in the data and do not include known graph properties in their inference process. This lowers the prediction accuracy of these methods, limiting their usability in practice. Results: We propose a post-processing algorithm which is applicable to any confidence ranking of regulatory interactions obtained from a network inference method which can use, inter alia, graphlets and several graph-invariant properties to re-rank the links into a more accurate prediction. To demonstrate the potential of our approach, we re-rank predictions of six different state-of-the-art algorithms using three simple network properties as optimization criteria and show that Netter can improve the predictions made on both artificially generated data as well as the DREAM4 and DREAM5 benchmarks. Additionally, the DREAM5 E. coli. community prediction inferred from real expression data is further improved. Furthermore, Netter compares favorably to other post-processing algorithms and is not restricted to correlation-like predictions. Lastly, we demonstrate that the performance increase is robust for a wide range of parameter settings. Netter is available at http://bioinformatics. intec. ugent. be. Conclusions: Network inference from high-throughput data is a long-standing challenge. In this work, we present Netter, which can further refine network predictions based on a set of user-defined graph properties. Netter is a flexible system which can be applied in unison with any method producing a ranking from omics data. It can be tailored to specific prior knowledge by expert users but can also be applied in general uses cases. Concluding, we believe that Netter is an interesting second step in the network inference process to further increase the quality of prediction

Strategies for multiobjective genetic algorithm development: Application to optimal batch plant design in process systems engineering

This work deals with multiobjective optimization problems using Genetic Algorithms (GA). A MultiObjective GA (MOGA) is proposed to solve multiobjective problems combining both continuous and discrete variables. This kind of problem is commonly found in chemical engineering since process design and operability involve structural and decisional choices as well as the determination of operating conditions. In this paper, a design of a basic MOGA which copes successfully with a range of typical chemical engineering optimization problems is considered and the key points of its architecture described in detail. Several performance tests are presented, based on the influence of bit ranging encoding in a chromosome. Four mathematical functions were used as a test bench. The MOGA was able to find the optimal solution for each objective function, as well as an important number of Pareto optimal solutions. Then, the results of two multiobjective case studies in batch plant design and retrofit were presented, showing the flexibility and adaptability of the MOGA to deal with various engineering problems

State-of-the-art in aerodynamic shape optimisation methods

Aerodynamic optimisation has become an indispensable component for any aerodynamic design over the past 60 years, with applications to aircraft, cars, trains, bridges, wind turbines, internal pipe flows, and cavities, among others, and is thus relevant in many facets of technology. With advancements in computational power, automated design optimisation procedures have become more competent, however, there is an ambiguity and bias throughout the literature with regards to relative performance of optimisation architectures and employed algorithms. This paper provides a well-balanced critical review of the dominant optimisation approaches that have been integrated with aerodynamic theory for the purpose of shape optimisation. A total of 229 papers, published in more than 120 journals and conference proceedings, have been classified into 6 different optimisation algorithm approaches. The material cited includes some of the most well-established authors and publications in the field of aerodynamic optimisation. This paper aims to eliminate bias toward certain algorithms by analysing the limitations, drawbacks, and the benefits of the most utilised optimisation approaches. This review provides comprehensive but straightforward insight for non-specialists and reference detailing the current state for specialist practitioners

Global design of analog cells using statistical optimization techniques

We present a methodology for automated sizing of analog cells using statistical optimization in a simulation based approach. This methodology enables us to design complex analog cells from scratch within reasonable CPU time. Three different specification types are covered: strong constraints on the electrical performance of the cells, weak constraints on this performance, and design objectives. A mathematical cost function is proposed and a bunch of heuristics is given to increase accuracy and reduce CPU time to minimize the cost function. A technique is also presented to yield designs with reduced variability in the performance parameters, under random variations of the transistor technological parameters. Several CMOS analog cells with complexity levels up to 48 transistors are designed for illustration. Measurements from fabricated prototypes demonstrate the suitability of the proposed methodology

Integrated system to perform surrogate based aerodynamic optimisation for high-lift airfoil

This work deals with the aerodynamics optimisation of a generic two-dimensional three element high-lift configuration. Although the high-lift system is applied only during take-off and landing in the low speed phase of the flight the cost efficiency of the airplane is strongly influenced by it [1]. The ultimate goal of an aircraft high lift system design team is to define the simplest configuration which, for prescribed constraints, will meet the take-off, climb, and landing requirements usually expressed in terms of maximum L/D and/or maximum CL. The ability of the calculation method to accurately predict changes in objective function value when gaps, overlaps and element deflections are varied is therefore critical. Despite advances in computer capacity, the enormous computational cost of running complex engineering simulations makes it impractical to rely exclusively on simulation for the purpose of design optimisation. To cut down the cost, surrogate models, also known as metamodels, are constructed from and then used in place of the actual simulation models. This work outlines the development of integrated systems to perform aerodynamics multi-objective optimisation for a three-element airfoil test case in high lift configuration, making use of surrogate models available in MACROS Generic Tools, which has been integrated in our design tool. Different metamodeling techniques have been compared based on multiple performance criteria. With MACROS is possible performing either optimisation of the model built with predefined training sample (GSO) or Iterative Surrogate-Based Optimization (SBO). In this first case the model is build independent from the optimisation and then use it as a black box in the optimisation process. In the second case is needed to provide the possibility to call CFD code from the optimisation process, and there is no need to build any model, it is being built internally during the optimisation process. Both approaches have been applied. A detailed analysis of the integrated design system, the methods as well as th

Locally Adaptive Optimization: Adaptive Seeding for Monotone Submodular Functions

The Adaptive Seeding problem is an algorithmic challenge motivated by influence maximization in social networks: One seeks to select among certain accessible nodes in a network, and then select, adaptively, among neighbors of those nodes as they become accessible in order to maximize a global objective function. More generally, adaptive seeding is a stochastic optimization framework where the choices in the first stage affect the realizations in the second stage, over which we aim to optimize. Our main result is a $(1-1/e)^2$-approximation for the adaptive seeding problem for any monotone submodular function. While adaptive policies are often approximated via non-adaptive policies, our algorithm is based on a novel method we call \emph{locally-adaptive} policies. These policies combine a non-adaptive global structure, with local adaptive optimizations. This method enables the $(1-1/e)^2$-approximation for general monotone submodular functions and circumvents some of the impossibilities associated with non-adaptive policies. We also introduce a fundamental problem in submodular optimization that may be of independent interest: given a ground set of elements where every element appears with some small probability, find a set of expected size at most $k$ that has the highest expected value over the realization of the elements. We show a surprising result: there are classes of monotone submodular functions (including coverage) that can be approximated almost optimally as the probability vanishes. For general monotone submodular functions we show via a reduction from \textsc{Planted-Clique} that approximations for this problem are not likely to be obtainable. This optimization problem is an important tool for adaptive seeding via non-adaptive policies, and its hardness motivates the introduction of \emph{locally-adaptive} policies we use in the main result

Group Leaders Optimization Algorithm

We present a new global optimization algorithm in which the influence of the leaders in social groups is used as an inspiration for the evolutionary technique which is designed into a group architecture. To demonstrate the efficiency of the method, a standard suite of single and multidimensional optimization functions along with the energies and the geometric structures of Lennard-Jones clusters are given as well as the application of the algorithm on quantum circuit design problems. We show that as an improvement over previous methods, the algorithm scales as N^2.5 for the Lennard-Jones clusters of N-particles. In addition, an efficient circuit design is shown for two qubit Grover search algorithm which is a quantum algorithm providing quadratic speed-up over the classical counterpart